Clyde were vying with Peterhead for the League Two title and automatic promotion until the final match of the regular season, despite being docked four points in March for fielding an ineligible player.
McNiff’s 60th-minute strike was added to four minutes from time by former Annan team-mate Ally Love, who assumed the penalty honours in the absence of injured fellow striker David Goodwillie.
And the defender, who works for a bank, had a little extra motivation against his former club after being told he could have time off if Clyde triumphed.
“I had to work hard to get this week off,” he said. “They told me that, if we won today, I would have next week off to go away with the boys to Spain.”